BIOB 272 1st EditionExam # 2 Study Guide Lectures: 13 - 23Lecture 13: Genome sequencing & physical maps (February 25) - Understand what is meant by polyploidy. Polyploidy: more than two sets of chromosomeso Common in plants, occasional in fish and amphibians and rare in mammalso Imp. over evolutionary history- whole genome duplications may provideraw material for adaptationo Odd ploidies (3N)= often sterile but 4N, etc ploidies are fertile and oftenhighly fito ** it is the BALANCE between the #of gene copies that is important for proper development, not necessarily the total number of gene copies (i.e two frogs shown in class)-Understand what is meant by chromosome deletions, duplications, inversions, and translocations, how these changes arise and how they influence genetic information in the genome. o **Chromosomal # can vary among similar specieso Deletion: loss of a chromosomal segment- effects depend on size of region losto Duplication: repeating of a chromosomal segment- May be deleterious, common in humans, can provide raw material for evolutionary innovation**Deletions and Duplications arise by similar mechanisms that involve errors in recombination= illegitimate recombination between direct repeats: homologous sequences in same orientation along chromosomeo Inversions: double breakage and insertion of flipped segmento Pericentric Inversion: includes centromere (flip around centromere)o Paracentric Inversion: does not include centromereo Translocations: reciprocal translocation between non-homologous chromosomeso Can result in chromosomal fusion= causing total chromosomal number to vary within a species (Mouse karyotype varies between 2N=40 to 2N=22)** Generally, inversions and translocations are not directly harmful to carriers, but their progenymay inherit deletions/duplications that are deleterious.i.e. Familial Down’s Syndrome: segment of chromosome 21 is translocated to chromosome 14 (3 copies total)- Key Points about chromosomal variation:o Variation in chromosome number and structure can have majoreffects on individual health and on evolutiono Aneuploidy - odd number of one chromosome common, harmful to individuals (e.g. trisomies)o Polyploidy - Duplication of all chromosomes common in many taxa, may result in changes in size or other traits, thought to contribute to speciationo Duplications – often raw material for adaptive evolutiono Deletions – usually deleterious (but progressive genome loss often part of adaptationto parasitic lifestyle!)o Inversions, translocations – not directly harmful, especially if balanced, no genome loss; adaptive potential= might affect offspring- Know the three kinds of genetic maps and how they are related.  Cytological Map: chromosome features based on microscopic image of chromosomes. Genetic/linkage map: linear arrangement of genes based on the analysis of recombination (crossing over) in crosses or pedigrees Physical (sequence) Map: Genome map based on determining the linear sequence of DNA Cytological Maps**Complete Genome Maps: includes info from genetic, linkage, cytological and physical sequence maps– Human Genome: 23 chromosomes (cytological map),3 billion basepairs (physical map),3,550 cM (linkage map)*– Women have a longer linkage map than men so average the male and female maps together -Know the four steps to sequencing a genome. What are the important steps of each? Understand the basic steps to Sanger sequencing.1. Obtain Genomic DNA sample- make a copy of the DNA using a process similar to what happens during mitosis (Sanger sequencing method)= relies on sequence termination:i. Chemical reaction that includes: DNA polymerase, DNA primer, nucleotide bases (A, T, G, C), Nucleotide bases that are ‘labeled’, addition of labeled bases stops reaction.ii. Repeated many times.2. Sequence genomic DNAo DNA separated by size using a gel and an electric currento DNA moves towards positive chargeo Shorter DNA moves faster= hierarchical, shotgun3. Assemble sequences in order o Based on finding regions of overlap between individual sequencing fragmentso VERY difficult for complex genomeso MOST rely on SHOTGUN approaches now4. Annotate Sequence-Understand the difference between hierarchical and shotgun genome sequencing. o Shotgun sequencing: randomly shears genomic DNA into small pieces which are cloned into plasmids and sequenced on both strands, thus eliminating the BAC step from the HGP's approach. Once the sequences are obtained, they are aligned and assembled into finished sequence.- more common with the Sanger Sequencingo Hierarchical Sequencing: genomic DNA is cut into pieces and inserted into BAC vectors. The BAC inserts are isolated and mapped to determine the order of each cloned fragment. Each BAC fragment is fragmented randomly into smaller pieces and each piece is cloned into a plasmid and sequenced on both strands. These sequences are aligned so that identical sequences are overlapping. These contiguouspieces are then assembled into finished sequence once each strand has been sequenced about 4 times to produce 8X coverage of high quality data.= has less mistakes-Understand how to calculate recombination rates from comparison of genetic and physical maps.o Genetic or Linkage map: linear arrangement of genes based on the analysis ofrecombination (crossing over) in crosses or pedigrees.o Physical (sequence) map: Genome map based on determining the linear sequence of DNA.o Linkage maps can be lined up with cytological maps of chromosome features and physical maps of the DNA sequence.o Recombination rate may vary across the genomeo A comparison of genetic and physical maps can be used to quantify variation in the average recombination rate between genomic regionscM/Mb= average rate of recombination- Need more than just the sequence of the genome:o Genome Annotation: identifying what part of DNA corresponds to genes, etc. Compare to known genes: Gene already described and sequencedExpressed Sequence Tags (EST), essentially randomly sequenced mRNA Predict genes:Computer predictionsLectures 14, 15 part Phylogenetics (March 2, 4)-Have a thorough understanding of what a phylogeny is how they are interpreted.o Phylogenies: branching diagram that represents a HYPOTHESIS on the evolutionary relationships among groups of organisms-Understand the difference between a rooted and unrooted tree. o Rooted tree: shows the most basal common ancestoro Unrooted tree: don’t imply a common ancestor-